Postmortem nasopharyngeal swabs performed during the COVID-19 infection: Analysis of preliminary clinical records by the genoa institute of legal medicine (North-West Italy)

COVID-19, the disease caused by the SARS-CoV-2 virus, is highly contagious. The persistence of the virus after infected individuals die remains unclear. This article reports the findings taken from postmortem nasopharyngeal swabs performed to investigate the presence of SARS-CoV-2 in the corpses transferred to the Genoa District Mortuary from the outset of the Italian lockdown (March 9) to the end of the first emergency phase (July 13). One hundred and eighty swabs were carried out: 13 corpses resulted positive for the virus, with the diagnosis being reached only after death. Seven were male and 6 female with an average age of 73.5 years old. The most frequent comorbidities recorded were arterial hypertension, diabetes, Alzheimer's, and pulmonary disease. In two cases, the swab tested positive at a distance of 125 h and 165 h from actual death. The nasopharyngeal swab results a useful way to screen corpses for COVID-19 and to handle bodies in Legal Medicine Centers where safe autoptic rooms are not available. Swabs are also a means of safeguarding forensic pathologists, identifying the presence of breeding grounds in the community and providing information for the Public Prosecutor's Office in legal cases. They are able to produce reliable results up to at least 7 days following death, provided that the corpse is correctly preserved.

A Comparison of Pharyngeal Swabs and Tracheal Secretions for the Diagnosing of COVID-19.

The aim of this study was to compare the test results from patients who, within a short timescale, have been tested for COVID-19 using both a pharyngeal swab and tracheal secretion. Data were collected from the database of AUH, from patients hospitalized between 1 March 2020 and 1 March 2021 who, due to symptoms of COVID-19, were tested by a pharyngeal swab and by tracheal secretion. We found great agreement between oropharyngeal swab and tracheal secretion RT-PCR testing for the diagnosis of COVID-19, with 98.5% of double tests being concordant and only 1.5% being discordant. This finding may advocate a single-test strategy being either an oropharyngeal swab RT-PCR testing or tracheal secretion, although this study revealed 15.9% false negative oropharyngeal swabs.

Exhaled breath condensate (EBC) for SARS-CoV-2 diagnosis still an open debate.

The real-time PCR (RT-PCR) on nasopharyngeal swabs (NPS) is the gold standard for the diagnosis of SARS-CoV-2. The exhaled breath condensate (EBC) is used to perform collection of biological fluid condensed in a refrigerated device from deep airways' exhaled air. We aimed to verify the presence of SARS-CoV-2 virus in the EBC from patients with confirmed SARS-CoV-2 infection by RT-PCR, and to determine if the EBC may represent a valid alternative to the NPS. Seventeen consecutive patients admitted to the Emergency Department of the Policlinico were enrolled in the present study with RT-PCR, clinical and radiological evidence of SARS-CoV-2. Within 24 h from the NPS collection the EBC collection was performed on SARS-CoV-2 positive patients. Informed written consent was gathered and the Ethic Committee approved the study. The mean age of patients was 60 years (24-92) and 64.7% (11/17) were male. Patient n.9 and n.17 died. All NPS resulted positive for SARS-CoV-2 at RT-PCR. RT-PCR on EBC resulted negative for all but one patients (patient n.12). In this study we did not find any correlation between positive NPS and the EBC in all but one patients enrolled. Based on these data which greatly differ from previous reports on the topic, this study opens several questions related to small differences in the complex process of EBC collection and how EBC could be really standardized for the diagnosis of SARS-CoV-2 infection. Further studies will be warranted to deepen this topic.

SARS-CoV-2 RNA Persistence in Naso-Pharyngeal Swabs.

Since February 2020, Italy has been seriously affected by the SARS-CoV-2 pandemic. To support the National Health Care system, naso-pharyngeal/oropharyngeal swabs collected from suspected cases of Teramo province, Abruzzo region, are tested at Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, for the presence of SARS-CoV-2 RNA. Out of 12,446 tested individuals, 605 returned positive results at least once, with prevalence significantly higher in men. A reduction of the level of viral RNA in the first swab per each positive patient collected over time was also observed. Moreover, 81 patients had at least one positive sample and two final negative tests: positivity in swabs lasted from 14 to 63 days, with a median value of 30 days. This shows the potential for the virus to coexist with patients for a long time, although we highlighted intermittent positivity in several cases. The evolution of the SARS-CoV-2 epidemiological situation and knowledge on viral shedding should be closely monitored, to interpret the findings correctly and adjust accordingly the surveillance activities.

Laryngotracheal aspiration test reduce the false negative rate in patients with suspected SARS-COV-2 pneumonia despite a negative nasopharyngeal swab.

BACKGROUND: In the emergency department (ED) definitive diagnosis of SARS-COV-2 pneumonia is challenging as nasopharyngeal swab (NPS) can give false negative results. Strategies to reduce false negative rate of NPS have limitations. Serial NPSs (24-48 h from one another) are time-consuming, sputum can not be collected in the majority of patients, and bronchoalveolar lavage (BAL), the most sensitive test, requires specific expertise. Laryngotracheal aspiration (LTA) is easy to perform and showed a similar accuracy to BAL for diagnosis of other pulmonary diseases, however it was not studied to diagnose SARS-COV-2 pneumonia. OBJECTIVE: An observational cross-sectional study was performed to evaluate the negative predictive value of LTA in patients with suspected SARS-COV-2 pneumonia despite a negative NPS. METHODS: In the EDs of two university hospitals, consecutive patients with suspected SARS-COV-2 pneumonia despite a negative NPS underwent LTA performed with a nasotracheal tube connected to a vacuum system. Final diagnosis based on all respiratory specimen tests (NPS, LTA and BAL) and hospital data was established by two reviewers and in case of discordance by a third reviewer. RESULTS: 117 patients were enrolled. LTA was feasible in all patients and no patients experienced adverse events. Fifteen (12.7%) patients were diagnosed with community-acquired SARS-COV-2 pneumonia: 13 LTA positive and only 2 (1.7%) LTA negative. The negative predictive value of NPS and LTA was 87.3% (79.9% - 92.7%) and 98.1% (93.3%99.8%) respectively. CONCLUSIONS: LTA resulted feasible, safe and reduced false negative rate in patients with suspected SARS-COV-2 pneumonia despite a negative NPS.

Epidemiological Significance of SARS-CoV-2 RNA Dynamic in Naso-Pharyngeal Swabs.

From 16 March to 15 December 2020, 132,357 naso-pharyngeal/oropharyngeal swabs were collected in the province of Teramo, Abruzzo Region, Italy, and tested for the presence of SARS-CoV-2 genomic RNA by a commercially available molecular assay. A total of 12,880 swabs resulted positive. For 8212 positive patients (4.150 women and 4.062 men) the median age was statistically different between women (median: 49.55 ± 23.9 of SD) and men (median: 48.35 ± 23.5 of SD) while no differences were found in the comparison between the cycle threshold for the N protein-encoding gene (CT N) median values and gender. Differences were observed in the CT N gene median values of swabs collected from March to September as well as in the pairwise comparison between September and October and between November and December. The CT N gene median values observed in specific periods characterizing the SARS-CoV-2 epidemic in 2020 were also compared with the incidence of COVID-19 cases; a strong inverse correlation was highlighted (Pearson correlation coefficient = -0.978). Our findings confirm the usefulness of the CT N values as an indirect detection parameter to monitor viral loads in the population.

Application of an optimized pharyngeal swab-assisted device in pharyngeal sampling for COVID-19 patients.

BACKGROUND: Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has triggered a global pandemic. Healthcare workers are placed at an elevated risk of nosocomial cross-infection from clinical exposure. One diagnostic criterion for COVID-19 is a positive result from a real-time reverse transcriptase-polymerase chain reaction (qRT-PCR) assay of pharyngeal swab specimens, which has been a routine procedure for healthcare workers during the outbreak. In the context of a global shortage of personal protective equipment (PPE), we aimed to lower the probability of clinical cross-infection without impacting the results of pharynx sampling through an optimized pharyngeal swab assisted device (OPAD). METHODS: To evaluate the efficacy and feasibility of an OPAD for the detection of SARS-CoV-2, 22 confirmed COVID-19 cases were enrolled in our self-controlled study. The results of two pharyngeal sampling qRT-PCR tests using the OPAD or the traditional method were recorded each. Clinical data including baseline characteristics, laboratory tests, and computed tomography (CT) results were also collected. The procedure duration and levels of pharynx exposure with the OPAD, and the diagnostic consistency between the OPAD and the traditional method for pharyngeal sampling qRT-PCR, were evaluated individually. Additionally, a questionnaire was designed for healthcare workers who had performed the pharyngeal swab to deepen our understanding of their attitude during their service on the frontline. RESULTS: In all 44 samplings (22 samples with each method), the qRT-PCR results of 18 pairs (81.82%) were consistent, while 3 (13.64%) were single positive with the OPAD. The positive rate was slightly higher with the OPAD (54.55%, 12/22) than with the traditional method (45.45%, 10/22). Using the OPAD, the average procedure duration of sampling was 30 s (30±13 s). Pharynx exposure was excellent in 21 subjects (95.45%, 21/22), which meant that the operator could acquire the swabs without difficulty. CONCLUSIONS: As the COVID-19 pandemic escalates, our OPAD has identical efficacy compared to the traditional method for pharyngeal swabs, and it can also contribute to protecting the safety of healthcare workers.

Pharyngeal sampling for PCR-testing in the investigation of SARS-COV-2 vertical transmission in pregnancy.

The novel COVID-19 global pandemic has raised, among many others, major concerns regarding the impact of infection during pregnancy. Current evidence suggests that vertical transmission from mother to baby, antenatally or intrapartum, does occur, but is uncommon. According to the published reports of infants born to COVID-19-affected mothers, as well as the anecdotal experience of current practices worldwide, it appears that investigations regarding the potential of SARS-COV-2 vertical transmission in pregnancy have so far been based, to a large extent, on PCR testing of neonatal pharyngeal swab samples. Given that the transplacental route of intrauterine transmission for SARS-COV-2 is less likely to immediately involve the upper respiratory tract of the newborn, contrary to what happens after birth, it would be advisable to include appropriate biological samples, such as cord blood, placenta, amniotic fluid and neonatal blood, along with the pharyngeal samples, in order to contribute significantly to such investigations. It is important to point out that negative PCR tests of neonatal pharyngeal samples do not exclude the possibility of intrauterine viral transmission, while positive pharyngeal swabs are more likely to reflect intrapartum or postpartum contaminants, rather than antenatal intrauterine transmission, in the absence of other criteria. Revision and enhancement of the so far prevailing practices appear important, in order to facilitate the development of good clinical practice for managing neonates and ensuring safety of families and healthcare providers.

Salivary SARS-CoV-2 antigen rapid detection: A prospective cohort study.

BACKGROUND AND AIM: SARS-CoV-2 quick testing is relevant for the containment of new pandemic waves. Antigen testing in self-collected saliva might be useful. We compared salivary and naso-pharyngeal swab (NPS) SARS-CoV-2 antigen detection by a rapid chemiluminescent assay (CLEIA) and two different point-of-care (POC) immunochromatographic assays, with results of molecular testing. METHODS: 234 patients were prospectively enrolled. Paired self-collected saliva (Salivette) and NPS were obtained to perform rRT-PCR, chemiluminescent (Lumipulse G) and POC (NPS: Fujirebio and Abbott; saliva: Fujirebio) for SARS-CoV-2 antigen detection. RESULTS: The overall agreement between NPS and saliva rRT-PCR was 78.7%, reaching 91.7% at the first week from symptoms. SARS-CoV-2 CLEIA antigen was highly accurate in distinguishing positive and negative NPS (ROC-AUC = 0.939, 95%CI:0.903-0.977), with 81.6% sensitivity and 93.8% specificity. This assay on saliva reached the optimal value within 7 days from symptoms onset (Sensitivity: 72%; Specificity: 97%). Saliva POC antigen was limited in sensitivity (13%), performing better in NPS (Sensitivity: 48% and 66%; Specificity: 100% and 99% for Espline and Abbott respectively), depending on viral loads. CONCLUSIONS: Self-collected saliva is a valid alternative to NPS for SARS-CoV-2 detection by molecular, but also by CLEIA antigen testing, which is therefore potentially useful for large scale screening.

Public health and clinical approach to proactive Prevalence of symptoms-based diagnosis of mild SARS-CoV-2 infection in southern Tuscany.

BACKGROUND: To date, it is unknown how many Italians have had or have a mild SARS-CoV-2 infection, because of the lack of epidemiological studies involving the general population. STUDY DESIGN: Aim of this study was to investigate the prevalence/incidence of a symptoms-based mild SARS-CoV-2 infection in southern Tuscany, by using an online survey. METHODS: An anonymous random middle-aged sample of 3,460 individuals completed the survey. A symptom-score ≥5, calculated on 195 patients with RT-PCR COVID-19 disease (sensitivity/specificity of 0.815/0.780 respectively) was used for the diagnosis. RESULTS: This cut-off highlighted that 12.3% of all the population might have had a SARS-CoV-2 infection, while 3.9% of them might have it at the time of the survey. Female sex (OR=1.334 [1.029-1.728]; p=0.030), obesity status (OR=1.961 [1.304-2.949]; p=0.001), asthma (OR=2.035 [1.433-2.890]; p=0.0001), autoim-mune diseases (OR=2.103 [1.381-3.201]; p=0.001), were all risk factors for showing mild SARS-CoV-2 infection. Instead, the elderly had a low probability to develop mild forms of the disease (OR=0.984 [0.975-0.994]; p=0.001). CONCLUSION: A remarkable number of subjects in Southern Tuscany may have already had a mild SARS-CoV-2 infection. Symptoms scores might be used to screen subjects with a suspected infection. Female sex, obesity, asthma, autoimmune diseases may be factors linked with mild forms of COVID-19 disease.

COVID-19 screening protocols for preoperative assessment of head and neck cancer patients candidate for elective surgery in the midst of the pandemic: A narrative review with comparison between two Italian institutions.

BACKGROUND: Preoperative screening had a key role in planning elective surgical activity for head and neck cancer (HNC) during the COVID-19 pandemic. METHODS: All patients undergoing surgery for HNC at two Italian referral hospitals (University of Padua and National Cancer Institute [NCI]) during the peak of the COVID-19 epidemic in Italy were included. Accuracy of screening protocols was assessed. RESULTS: In the Padua protocol, 41 patients were screened by pharyngeal swab. The entire sample (100%) was admitted to surgery, diagnostic accuracy was 100%. In the NCI protocol, 23 patients underwent a telephone interview, blood test, and chest CT. Twenty patients (87%) were negative and were directly admitted to surgery. In the remaining 3 (13%), pharyngeal swab was performed. The screening was repeated until a negative chest CT was found. Diagnostic accuracy was 85%. CONCLUSIONS: Dedicated screening protocols for COVID-19 allow to safely perform elective HNC surgery.

Is naso-pharyngeal swab always safe for SARS-CoV-2 testing? An unusual, accidental foreign body swallowing.

Long and sharp objects can be foreign body intentionally or accidentally ingested. Timing of endoscopy relies on foreign body shape and size, localization in gastrointestinal tract, patient's clinical conditions, occurrence of symptoms, or onset of complications. We present a case of a 47-year-old male with no known comorbidity, who accidentally swallowed a portion of a naso-pharyngeal swab half-broken during the second diagnostic test for SARS-CoV-2. The intact swab had a total length of 15 cm and was made of wood. The patient was asymptomatic, laboratory tests were normal, and neck-chest-abdominal X-ray and CT scan were negative for major complications. Upper gastrointestinal endoscopy was promptly performed to prevent the long sharp swab from crossing the pylorus leading to serious complications and, therefore, risk surgical intervention. The patient was intubated and the procedure was carried out under general anesthesia. In the gastric body, broken naso-pharyngeal swab was detected among the food debris, and using a latex rubber hood, the 7.5 cm foreign body was removed with a retrieval alligator-tooth forceps. Our hospital is located in a high-risk area of COVID-19 outbreak where many naso-pharyngeal swabs are performed, and to our knowledge, this is the first report of swab ingestion during SARS-CoV-2 test.

SARS-CoV-2 identification and IgA antibodies in saliva: One sample two tests approach for diagnosis.

AIM: This study aims to verify whether standardized saliva collection is suitable for SARS-CoV-2 molecular detection and IgA measurement. METHODS: 43 COVID-19 inpatients and 326 screening subjects underwent naso-pharyngeal (NP)-swab and saliva collection (Salivette). Inpatients also underwent repeated blood collections to evaluate inflammation and organs involvement. In all patients and subjects, SARS-CoV-2 (gene E) rRT-PCR was undertaken in saliva and NP-swabs. Salivary IgA and serum IgA, IgG, IgM were measured on inpatients' samples. RESULTS: NP-swabs and saliva were both SARS-CoV-2 positive in 7 (16%) or both negative in 35 (82%) out of 43 patients successfully included in the study. NP-swabs and saliva results did not perfectly match in one patient (saliva positive, NP-swab negative). Positive molecular results were significantly associated with disease duration (p = 0.0049). 326/326 screening subjects were SARS-CoV-2 negative on both NP-swabs and saliva. Among the 27 saliva samples tested for IgA, 18 were IgA positive. Salivary IgA positivity was associated with pneumonia (p = 0.002) and CRP values (p = 0.0183), not with other clinical and molecular data, or with serum immunoglubulins. CONCLUSIONS: A standardized saliva collection can be adopted to detect SARS-CoV-2 infection in alternative to NP-swabs. Preliminary data on salivary IgA support the use of saliva also for patient monitoring.

COVID-19 challenge: proactive management of a Tertiary University Hospital in Veneto Region, Italy.

BACKGROUND: The aim of this study is to describe the successful emergency plan implemented by Padova University Hospital (AOUP) during the COVID-19 pandemic. METHODS: The emergency plan included early implementation of procedures aimed at meeting the increasing demand for testing and care while ensuring safe and timely care of all patients and guaranteeing the safety of healthcare workers. RESULTS: From 21 February to 1 May 2020, there were 3,862 confirmed cases of SARS-CoV-2 infection in the Province of Padua. A total of 485 patients were hospitalized in AOUP, of which 91 were admitted to the ICU; 12 .6% of admitted patients died. The average bed occupancy rate in the ICU was 61.1% (IQR 43.6%:77.4%). Inpatient surgery and inpatient admissions were kept for 76% and 74%, respectively, compared to March 2019. A total of 123,077 swabs were performed, 19.3% of which (23,725 swabs) to screen AOUP workers. The screening of all staff showed that 137 of 7,649 (1.8%) hospital workers were positive. No healthcare worker died. DISCUSSION: AOUP strategy demonstrated effective management of the epidemic thanks to the timely implementation of emergency procedures, a well-coordinated effort shared by all hospital Departments, and their continuous adjustment to the ongoing epidemic. Timely screening of all hospital workers proved to be particularly important to defend the hospital, avoiding epidemic clusters due to unknown positive cases.

Report of Positive Placental Swabs for SARS-CoV-2 in an Asymptomatic Pregnant Woman with COVID-19.

Currently, limited data on maternal and neonatal outcomes of pregnant women with infection and pneumonia related to SARS coronavirus 2 (SARS-CoV-2) are available. Our report aims to describe a case of placental swabs positive for the molecular research on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 RNA in an asymptomatic woman with positive rhino-pharyngeal swab for SARS-CoV-2 who underwent an urgent cesarean section in our obstetrics unit. Sample collection, processing, and laboratory testing were conducted in accordance with the World Health Organization (WHO) guidance. In the next months, conclusive data on obstetrical outcomes concerning the gestational age and pregnancy comorbidity as well as the eventual maternal-fetal transmission are needed.

A Case of COVID-19 Patient with False-Negative for SARS-CoV-2 of Pharyngeal Swab, from a Chinese Traveller Returning from Wuhan, Hubei Province, China, January 2020.

We report a case of coronavirus disease (COVID-19) in a Japanese patient with a false-negative result in the reverse-transcription polymerase chain reaction for severe acute respiratory syndrome coronavirus 2 detection in the pharyngeal swab. The patient had acquired the infection from a Chinese traveler returning from Wuhan, Hubei Province, China. If a patient is clinically or epidemiologically suspected with COVID-19, appropriate infection and prevention control measures such as standard, contact, and droplet precaution are necessary until the patient is proven to have a true-negative result.

Study of SARS-CoV-2 in semen and urine samples of a volunteer with positive naso-pharyngeal swab.

INTRODUCTION: The recent appearance of SARS-CoV-2 in Wuhan in 2019 has started a pandemic which has involved over a million people worldwide. A matter of debate is the possible viral detection in different body fluids than respiratory droplets. Thus, we evaluated the possible presence of SARS-CoV-2 in semen and urine samples of a volunteer with confirmed COVID-19. MATERIALS AND METHODS: A 31-year-old man with fever, myalgia, anosmia, and ageusia was tested and found positive for SARS-CoV-2 through a pharyngeal swab. Eight days after he provided semen and urine samples in which viral RNA presence was measured using a Real time RT PCR system (RealStar SARS-CoV-2 RT-PCR, Altona Diagnostics) targeting E and S viral genes. RESULTS AND DISCUSSION: Semen and urine samples search for SARS-CoV-2 RNA was negative. Although this should be interpreted cautiously, it may be possible that either the viral clearance kinetics in these matrices matches the progressive clinical recovery of the patient or that the virus was never present in these fluids at the time of the laboratory diagnosis.

Detectable 2019-nCoV viral RNA in blood is a strong indicator for the further clinical severity.

The novel coronavirus (2019-nCoV) infection caused pneumonia. we retrospectively analyzed the virus presence in the pharyngeal swab, blood, and the anal swab detected by real-time PCR in the clinical lab. Unexpectedly, the 2109-nCoV RNA was readily detected in the blood (6 of 57 patients) and the anal swabs (11 of 28 patients). Importantly, all of the 6 patients with detectable viral RNA in the blood cohort progressed to severe symptom stage, indicating a strong correlation of serum viral RNA with the disease severity (p-value = 0.0001). Meanwhile, 8 of the 11 patients with annal swab virus-positive was in severe clinical stage. However, the concentration of viral RNA in the anal swab (Ct value = 24 + 39) was higher than in the blood (Ct value = 34 + 39) from patient 2, suggesting that the virus might replicate in the digestive tract. Altogether, our results confirmed the presence of virus RNA in extra-pulmonary sites.